Fighting a 2009 assessment for client and client shows refund on 2011 return

Facts -
Client contacted me to file her 2011 return, and also showed me the 90- day notice regarding a 2009 assessment (the 90 days had passed when she showed it to me).
Client's assessment for 2009 was about $3800, but based on information she gave me, I believe she only owes $1800 (she is eligible for an education credit of $2000). I have written to the Reconsideration Unit, given them this information and explained this whole situation.
Client's return for 2011 shows a refund of $2400, but I have not filed it yet because I know it would automatically be applied against the 2009 assessment.
Assuming the Reconsideration Unit accepts her information and I am successful in reducing the 2009 assessment down to $1800, is it safe to file the 2011 return and let the IRS apply the refund to the $1800 balance owed and send the remaining $600 to her? Or is she better off borrowing and paying $1800 for 2009 and then waiting for her full 2011 refund after that?
Thanks in advance.
Chris A Johnson, EA
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